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Stanford University
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3MATRIX for 3D Visualization of Drug Targets
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The 3MOTIF and 3MATRIX Suites of software enable visualization and 3-dimensional manipulation of discrete sequence motifs found in protein structures. The software enables drug target analysis by exposing characteristics of these conserved regions, such as solvent accessible surface area. The software uses a color scheme to convey a motif's physical properties in a way that can be easily interpret...
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Stanford University
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3MOTIF for 3D Visualization of Drug Targets
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The 3MOTIF and 3MATRIX Suites of software enable visualization and 3-dimensional manipulation of discrete sequence motifs found in protein structures. The software enables drug target analysis by exposing characteristics of these conserved regions, such as solvent accessible surface area. The software uses a color scheme to convey a motif's physical properties in a way that can be easily interpret...
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Stanford University
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A Live Cell Fluorescent Mitosis Biosensor
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Professor Tobias Meyer, Joshua Jones, and Angie Hahn at Stanford have developed the first live cell biosensor-based fluorescent imaging strategy to quantitatively analyze the timing of the cell cycle phases, M, G1, S, and G2. The cell cycle is a tightly regulated cellular process and failure at critical checkpoints within often results in genetic instability and eventually, cancer. In high content...
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University of California, Irvine
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A Method For Detecting Interactions Between Protein, Encoded By cDNAs And Any Defined Molecular Target
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Researchers at the University of California, Irvine, have designed a sensitive, high-throughput strategy that can be performed manually or by automation for detecting interactions between proteins, encoded by CDNAs and any defined molecular target including other proteins, nucleic acids, protein nucleic acid complexes and drug/protein/nucleic acid complexes. The components of this process include ...
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University of California, Irvine
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A Micro-Fluidic Platform for Performing Gel Electrophoresis and Western Analysis
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The Researchers at the University of California are developing a miniaturized, integrated microfluidic device and method ("lab on a chip") that performs gel electrophoresis followed by Western analysis. The technology utilizes a novel design where a single channel serves multiple purposes, including (1) cooling, (2) staining, (3) detaining, (4) electro-blotting.The current invention provides multi...
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University of California, Irvine
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A Micro-Platform for Solubility Characterization of Induced Protein in Cells
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Researchers at the University of California are developing a miniaturized, integrated apparatus and method for incubating cells and performing solubility characterization of induced soluble protein in cells at regular, pre-programmed intervals. This invention provides an integrated, automated way to test cells for soluble protein content during incubation. The apparatus, which is small enough to f...
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University of California, Irvine
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A Micro-Platform for the Production of Plasmid Constructs, Cell Transformation, and Validation
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Researchers at the University of California are developing a micro-platfom device which miniaturizes and incorporates the gene expression optimization procedures on a lab-on-a-chip. Specifically, the technology integrates distinct laboratory steps onto a single automated platform that uses microliters of sample. These steps are the insertion of a PCR product into a plasmid (ligation reaction), the...
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University of California, Irvine
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A Microfluidic Device for Gel Electrophoresis with Integrated Thermal Cycling and Sample Elution
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University of California, Irvine researchers are developing a new microfluidic device and method for performing rapid thermal cycling on a small quantity of DNA sample for the purpose of performing PCR. This is followed by purification of the amplified DNA and then an optional step is available on this device to elute a specific band of purified DNA.Compared to currently known microfluidic devices...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Berkeley
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A New Process for Biomolecule Patterning
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Patterning of biomolecules is important in areas like biological analysis, diagnostics and genomics. In addition, molecular patterning could be useful for spatial control of various surface properties such as hydrophobicity and surface charge.Currently, molecules are patterned using lithography, stamping, or using scanning tips. Lithography requires either specially synthesized light-sensitive mol...
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University of California, Irvine
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A New Tandem-Affinity Tag for Two-Step Protein Purification under Fully Denaturing Conditions
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University of California, Irvine researchers have developed a novel tandem-affinity tag that is compatible with two-step purification under fully denaturing conditions such as 8 M urea or 6 M guanidinium. This novel tag serves as a biotinylation signal in vivo. Tagged proteins are efficiently biotinylated in vivo in both yeast and mammalian cells at a specific lysine residue present in the tag. Th...
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Stanford University
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A new technology for barcoded clonal amplification
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Here we describe a process for bar-coding and clonal amplification of DNA from the same or different sources. The proposed technique can be used for genome sequencing, expression profiling, sequencing of selected pieces of DNA from genome or microbial flora typing. Single nucleic acid molecule is captured and clonally amplified for sequence analysis. Using this technique thousands of DNA molecule ...
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University of California, Berkeley
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A UNIVERSAL, LIGHT-SWITCHABLE GENE PROMOTER SYSTEM
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Synopsis:This invention consists of an artificial promoter system that can be fused upstream of any desired gene, enabling reversible and light-switchable induction or repression of gene expression in any suitable host cell.New data to be filed in a provisional patent application demonstrates optimized expression conditionsand a "switching off" mechanism in addition to the "switching on" mechanism...
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University of California, Berkeley
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A UNIVERSAL, LIGHT-SWITCHABLE GENE PROMOTER SYSTEM
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Synopsis:This invention consists of an artificial promoter system that can be fused upstream of any desired gene, enabling reversible and light-switchable induction or repression of gene expression in any suitable host cell.New data to be filed in a provisional patent application demonstrates optimized expression conditionsand a "switching off" mechanism in addition to the "switching on" mechanism...
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University of California, Berkeley
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A UNIVERSAL, LIGHT-SWITCHABLE GENE PROMOTER SYSTEM
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Synopsis:This invention consists of an artificial promoter system that can be fused upstream of any desired gene, enabling reversible and light-switchable induction or repression of gene expression in any suitable host cell.New data to be filed in a provisional patent application demonstrates optimized expression conditionsand a "switching off" mechanism in addition to the "switching on" mechanism...
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University of California, Berkeley
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A UNIVERSAL, LIGHT-SWITCHABLE GENE PROMOTER SYSTEM
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Synopsis:This invention consists of an artificial promoter system that can be fused upstream of any desired gene, enabling reversible and light-switchable induction or repression of gene expression in any suitable host cell.New data to be filed in a provisional patent application demonstrates optimized expression conditionsand a "switching off" mechanism in addition to the "switching on" mechanism...
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Stanford University
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Analysis of Quantitative PCR
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This invention provides mathematical methods and techniques for accurate prediction, analysis, and estimation of Polymerase Chain Reaction (PCR) based biochemical processes in the field of Genomics. The techniques presented in this invention can be implemented to analyze the results of Polymerase-based biochemical processes such as QPCR assays and statistically estimate the absolute and/or relativ...
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University of California, San Diego
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Arrays for Functional Genomics/High Throughput Phenotyping
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UCSD researchers have developed a method for assembling live biological cells using electrokinetic addressing for functional genomics studies. The method employs rapid, single cell arraying with real time fluorescence monitoring, in a non-well format and w...
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Stanford University
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Charge Alternation DNA Detection System
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This invention introduces a novel method for rapid detection and identification of DNA sequences present in a biological sample. The DNA identification is achieved by detection of electric charge perturbations of polymerase-catalyzed reaction by the electrochemical detection sensor with immobilized DNA. This invention provides rapid and sensitive detection of biological pathogens, genetic mutation...
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Stanford University
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Charge Sequencing: A New Technique for DNA Sequencing and SNP Detection
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By detecting variations in the charge of immobilized DNA, this novel technique is a faster and cheaper alternative to current methods of DNA sequencing. Developed at the Stanford Genome and Technology Center, the electrostatic scanning technique uses magnetically immobilized strands of DNA to read the genetic code. One possible application of this invention is to integrate it onto a silicon wafer....
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Stanford University
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Chromosomal Recombination in Somatic Cells to Create Mouse Models for Different Human Diseases
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Stanford scientists developed a novel method to generate site-directed chromosome recombination in somatic cells in mice. Using this technology it is possible to manipulate mammalian genomes in somatic cells and to specifically label the homozygous mutant cells in an otherwise heterozygous animal. The recombinantion of the chromosomes during the somatic state is regulated by Cre recombinase and th...
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Stanford University
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Classification of Patients Having Diffuse Large B-Cell Lymphoma Based on Gene Expression
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Stanford researchers have developed an assay for subtyping diffuse large B-cell lymphoma (DLBCL) patients based upon the gene expression profiles in DLBCL sample tissue. The method involves the correlation of gene expression in tumor samples from DLBCL patients for the classification of disease characteristics such as patient survival. From this analysis, the expression level of a set of six genes...
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Stanford University
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Clinical and Genomic/Proteomic Data Integration and QA/QC Analysis System
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Using open-source tools, the Stanford researchers Ji, Kumm and Davis have developed a highly cost-effective, flexible and web-oriented software system to conduct real-time quality assurance/quality control (QA/QC) analysis on genomic and proteomic data sets generated from clinical studies. This system enables reproducible biomarker discovery by conducting on-the-fly analysis for a variety of metri...
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University of California, Berkeley
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Combinatorial Purine Libraries as Inhibitors of Cyclin Dependent Kinases
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Abstract:Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were iden...
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University of California, Berkeley
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Combinatorial Purine Libraries as Inhibitors of Cyclin Dependent Kinases
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Abstract:Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors of the human CDK2-cyclin A kinase complex and of Saccharomyces cerevisiae Cdc28p were iden...
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Stanford University
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Conditional Gene Overexpression for Therapeutic & Diagnostic Targets
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To better model human disease, the inventors have developed a conditional strategy for regulating gene expression in a tissue-specific and developmental manner. The Tetracycline Regulatory System (tet system) is used to conditionally overexpress the oncogene MYC. This allowed for determination of a direct correlation between increasing amounts of doxycycline and MYC expression. The inventors have ...
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Stanford University
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Cystic Fibrosis (CF) Arrayed Primer
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By means of arrayed single primer nucleotide extension (APEX) technology, we have designed a genotyping microarray with 204 probe sites for Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) mutation detection. The APEX array, based on a platform technology for disease detection with multiple applications, is a robust, cost-effective, and easily modifiable assay suitable for CF carrier scr...
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Stanford University
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Detection of Protein Modification
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This invention provides methods for detecting molecular interactions, particularly protein-protein interactions, in eukaryotic and mammalian cells, in situ or in vitro using at least two inactive, weakly-complementing beta-lactamase fragments, which form fusion proteins with the molecules of interest. The detection of molecular interactions in mammalian cells is not limited to the nuclear compartm...
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University of California, Irvine
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Development of Diagnostics and Therapeutics for Cornelia de Lange Syndrome
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The product of the NIPBL gene is a global regulator of DNA interactions that control the expression of many classes of genes. It is believed that the abnormalities of CdLS arise because levels and sites of expression of many genes change when NIPBL levels are low. University of California, Irvine researchers have developed a mouse model of CdLS, based on heterozygous mutation of the NIPBL gene, an...
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Stanford University
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DNA Fragment Identification System based on Magnetic Nanoparticles
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The development of high sensitivity, quantitative DNA fragment detection and identification systems has been of growing importance in the fields of functional genomics, forensics, bio-defense, anti-bioterrorism, and other biotechnology applications. However, virtually all DNA fragment detection systems used today rely on fluorescent detection, which can be very costly. Researchers at Stanford have...
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University of California, Berkeley
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DNA RECOMBINATION IN EUKARYOTIC CELLS BY THE BACTERIOPHAGE PHIC31 RECOMBINATION SYSTEM
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This invention provides methods for obtaining specific and stable integration of nucleic acids into eukaryotic cells. The method is an alternative to the widely used CRE-LOX method.The invention makes use of site-specific recombination systems that use prokaryotic recombinase polypeptides, such as the phiC31 recombinase, that can mediate recombination between the recombination sites, but not betwe...
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University of California, Berkeley
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DNA RECOMBINATION IN EUKARYOTIC CELLS BY THE BACTERIOPHAGE PHIC31 RECOMBINATION SYSTEM
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This invention provides methods for obtaining specific and stable integration of nucleic acids into eukaryotic cells. The method is an alternative to the widely used CRE-LOX method.The invention makes use of site-specific recombination systems that use prokaryotic recombinase polypeptides, such as the phiC31 recombinase, that can mediate recombination between the recombination sites, but not betwe...
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University of California, Berkeley
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DNA RECOMBINATION IN EUKARYOTIC CELLS BY THE BACTERIOPHAGE PHIC31 RECOMBINATION SYSTEM
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This invention provides methods for obtaining specific and stable integration of nucleic acids into eukaryotic cells. The method is an alternative to the widely used CRE-LOX method.The invention makes use of site-specific recombination systems that use prokaryotic recombinase polypeptides, such as the phiC31 recombinase, that can mediate recombination between the recombination sites, but not betwe...
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Stanford University
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eBAS-3.5.0 (eMOTIF Batch Analysis Suite-3.5.0)
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eBAS-3.5.0 accepts FASTA-formatted ORFs, FASTA-formatted genomic sequences, and FASTA-formatted protein sequences as input. ORFs, in the context of eBAS-3.5.0, are DNA sequences that code for proteins. Assuming that the ORFs are reported in the right frame, eBAS-3.5.0 will only translate one frame of an ORF's DNA sequence. Genomic sequences, in the context of eBAS-3.5.0, are DNA sequences that may...
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University of California, Berkeley
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Elves--An Expert System for X-ray Crystallography of Biological Macromolecules
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Elves is a computer expert system for X-ray crystallography of biological macromolecules. Elves automates and accelerates every step of X-ray data analysis, from processing X-ray diffraction images to guiding and refining a molecular model. Elves requires the use of CCP4, which must be obtained under separate license from a third party. Elves also uses common data analysis programs such as Mosflm....
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University of California, Berkeley
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Elves--An Expert System for X-ray Crystallography of Biological Macromolecules
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Elves is a computer expert system for X-ray crystallography of biological macromolecules. Elves automates and accelerates every step of X-ray data analysis, from processing X-ray diffraction images to guiding and refining a molecular model. Elves requires the use of CCP4, which must be obtained under separate license from a third party. Elves also uses common data analysis programs such as Mosflm....
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University of California, Berkeley
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Elves--An Expert System for X-ray Crystallography of Biological Macromolecules
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Elves is a computer expert system for X-ray crystallography of biological macromolecules. Elves automates and accelerates every step of X-ray data analysis, from processing X-ray diffraction images to guiding and refining a molecular model. Elves requires the use of CCP4, which must be obtained under separate license from a third party. Elves also uses common data analysis programs such as Mosflm....
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Stanford University
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eMOTIF v3.5.1 / eMOTIF Package
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*** NEW RELEASE, March 5, 2002: eMOTIF VERSION 3.6 NOW AVAILABLE***eMOTIF-Search, eMOTIF-Scan and eMOTIF-Maker are computer-based tools for protein identification and functionality.EMOTIF is a novel way of characterizing a group of functionally equivalent proteins. It generates descriptions in the form of allowable amino acids for each position in an active site, based on ungapped alignments of kn...
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Stanford University
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Fibroblast serum response predicts human cancer progression
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Stanford researchers have identified a set of genes representing the wound healing response also present in invasive cancers. More specifically, the wound response signature is a powerful prognostic indicator in breast cancer.The researchers have shown that the wound signature provides improved risk prediction compared to traditional criteria, illustrating the potential utility and improved risk s...
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Stanford University
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Fluorescently-tagged ribosomes to monitor conformational changes and ligand binding during translation.
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Despite the ribosome's biological and therapeutic importance, it remains very cumbersome to monitor ribosome activity. The current invention allows more facile investigation of ribosome activity by fluorescence spectroscopy. The modified ribosomes are prepared using specific steps to yield fluorescently tagged ribosomes.The labeling reagent could be incorporated into cell growth media and are rapi...
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Stanford University
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FSH and LH receptors or "High Level Expression of Soluble Gonadotropin Receptors"
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LH and FSH receptors belong to a sub-family of G-protein-coupled receptors with seven transmembrane alpha-helical regions and a large extracellular domain containing leucine-rich repeats. Recent isolation of cDNAs for human LH and FSH receptors allow for functional analysis in transfected cells. However, while truncated gonadotropin receptors containing only the extracellular region retain their l...
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Stanford University
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GABRIEL: a machine-learning system that incorporates expert knowledge into rules that analyze genetic data
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The GABRIEL (Genetic Analysis By Rules Incorporating Expert Logic) system of computer programs incorporates domain-specific and problem-solving expert knowledge into a series of rules that analyze and interpret data from DNA microarrays consistently and uniformly, A consultation module interprets data, an explanation module indicates the basis for decisions, and a rule-acquisition module allows us...
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University of California, Davis
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Gallic Acid Biosynthetic Pathway for Inhibiting the Production of Aflatoxins by A. flavus
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An established chemical production pathway for a compound, gallic acid, which can contribute to the reduction of aflatoxin contamination, has been identified by University of California, Davis researchers. Infection of agricultural crops by specific strains of the fungus Aspergillus flavus results in the production and accumulation of certain types of noxious compounds known as aflatoxins. Aflatox...
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Stanford University
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Gene Cloning Method
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Stanford and John Innes Centre researchers have developed a new cloning method that uses microarrays to rapidly identify and clone genes that contain mutations or different alleles of interest. Positional cloning can be a laborious process, even with organisms whose genomes have been fully sequenced. With organisms where only partial genome-sequences are available and in particular with those that...
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University of California, Berkeley
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Generalized Pair Hidden Markov Models for Alignment and Gene Finding
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Hidden Markov Models (HMMs) have been successfully applied to a variety of problems in molecular biology ranging from alignment problems to gene finding and annotation. Alignment problems can be solved with pair HMMs, while gene finding programs rely on generalized HMMs in order to model exon lengths.Researchers at the University of California, Berkeley have developed generalized pair HMMs, an ext...
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University of California, Berkeley
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Generalized Pair Hidden Markov Models for Alignment and Gene Finding
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Hidden Markov Models (HMMs) have been successfully applied to a variety of problems in molecular biology ranging from alignment problems to gene finding and annotation. Alignment problems can be solved with pair HMMs, while gene finding programs rely on generalized HMMs in order to model exon lengths.Researchers at the University of California, Berkeley have developed generalized pair HMMs, an ext...
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University of California, Berkeley
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GENES REGULATED IN RESPONSE TO LIGHT
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Light is a critical environmental factor for plants. It provides not only the energy for plant growth but also key informational signals that plants use to adapt and optimize growth morphology, fruiting, and formation of storage organs. The invention provides a method to identify nucleotide sequences regulated in response to light. The invention also provides a variety of expression vectors useful...
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University of California, Berkeley
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GENES REGULATED IN RESPONSE TO LIGHT
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Light is a critical environmental factor for plants. It provides not only the energy for plant growth but also key informational signals that plants use to adapt and optimize growth morphology, fruiting, and formation of storage organs. The invention provides a method to identify nucleotide sequences regulated in response to light. The invention also provides a variety of expression vectors useful...
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University of California, Berkeley
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GENES REGULATED IN RESPONSE TO LIGHT
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Light is a critical environmental factor for plants. It provides not only the energy for plant growth but also key informational signals that plants use to adapt and optimize growth morphology, fruiting, and formation of storage organs. The invention provides a method to identify nucleotide sequences regulated in response to light. The invention also provides a variety of expression vectors useful...
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Stanford University
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Genome wide analysis of protein synthesis
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Current methods of gene expression analysis can determine the genome-wide levels of individual mRNAs, which are then assumed to correlate with the final amounts of proteins expressed. However, in many cases, translation of mRNA by the ribosome has been shown to be dependent on the sequence and structure of the mRNA. Current methods of genome-wide analysis of protein synthesis ignore the subtleties...
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Stanford University
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GenomeScan
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GenomeScan is a program for identifying the exon-intron structures of genes in genomic DNA sequences from a variety of organisms, with a focus on human and other vertebrates. The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits. The input to the program consists of a genomic s...
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University of California, Davis
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Helicobacter Diagnostic Antigens for Mice
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Unique and immunoreactive murine (mouse) Helicobacter bilis recombinant antigens have been discovered by University of California, Davis researchers. H. Bilis infection is a widespread maintenance issue in research mouse colonies. Nearly 30 million mice are used annually for biomedical research, and mice are the predominant mammalian models in genomics research, making the potential market for rod...
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Stanford University
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Inducible Protein Stabilization Using Small Molecules
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This technology provides the ability to conditionally regulate fusion proteins using generic small molecules. Target proteins are fused with a small polypeptide tag, termed FRB*. As a result, the target protein becomes destabilized and is targeted for proteasomal degradation. In the presence of a synthetic analogue of rapamycin, the fusion protein binds FKBP12, rapidly restoring target protein sta...
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Stanford University
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Keratin Mutations May Predispose to Liver Diseases
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Keratins comprise a group of intermediate-filament cytoskeletal proteins and, in addition to their cytoprotective role, serve as important cell type-specific markers. Keratin mutations are associated with several skin-, oral-, esophageal-, ocular- and liver-related diseases that reflect tissue-specific expression of the particular keratin involved. From the 20+ keratin members (K1-K20), the kerati...
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Stanford University
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KNNimpute algorithm for estimation of missing values for microarray data
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Gene expression microarray experiments can generate data sets with multiple missing expression values. Unfortunately, many algorithms for gene expression analysis require a complete matrix of gene array values as input (for example Principal Components Analysis). In addition, methods such as hierarchical clustering and K-means clustering are not robust to missing data, and may lose effectiveness e...
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University of California, Irvine
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LEF-1 Internal Ribosome Entry Site
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University of California, Irvine researchers have found that LEF-1 mRNA exhibits internal ribosome entry site (IRES) activity through DNA and RNA transfections of a dicistronic vector containing the LEF-1 5' UTR sequences. Researchers found that the 5' UTR of human LEF-1 mRNA contains two independent IRES modules that are additive in their mediation of cap-independent translation of full length LE...
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University of California, Berkeley
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Lethal White Foal Allele
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Researchers at the University of California at Berkeley have developed an invention that tests for the presence of the lethal white foal allele. The DNA test identifies horses with the "lethal white overo" gene. The gene is responsible for lethal white foal syndrome, a recessive disorder of the intestinal tract that causes death of affected foals within 48 hours after birth. Horse breeders of: Pai...
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University of California, Berkeley
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Lethal White Foal Allele
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Researchers at the University of California at Berkeley have developed an invention that tests for the presence of the lethal white foal allele. The DNA test identifies horses with the "lethal white overo" gene. The gene is responsible for lethal white foal syndrome, a recessive disorder of the intestinal tract that causes death of affected foals within 48 hours after birth. Horse breeders of: Pai...
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Stanford University
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Magnetic Microarray IC Chip Designs
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Stanford researchers have developed a novel biosensor technology using a magnetic detection scheme. The chip design provides for high sensitivity and rapid response in detecting small numbers of biomolecules in arrays with up to 1 million probes. ...
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University of California, San Diego
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Method for Automated Injection of drosophila Embryos
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In order to facilitate high-throughput biology, genomics and functional proteomics studies using drosophila melanogaster (Fruit Fly), UCSD researchers have devised a device for rapid, large-scale microinjection of large numbers of drosophila embryos with t...
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University of California, Berkeley
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Method for NORMALIZING AND AMPLIFYING RNA
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The invention provides methods and compositions for normalizing and amplifying RNA populations. The methods generally comprise the steps OF : (a) copying MRNA to form first ss-cDNA; (b) converting the first ss-cDNA to first ds-cDNA; (C) linearly amplifying the first ds-cDNA to form first ARNA ; (d) tagging the 3'end of the first ARNA with a known sequence to form 3'-tagged first ARNA ; (e) copying...
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University of California, Berkeley
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Method for NORMALIZING AND AMPLIFYING RNA
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The invention provides methods and compositions for normalizing and amplifying RNA populations. The methods generally comprise the steps OF : (a) copying MRNA to form first ss-cDNA; (b) converting the first ss-cDNA to first ds-cDNA; (C) linearly amplifying the first ds-cDNA to form first ARNA ; (d) tagging the 3'end of the first ARNA with a known sequence to form 3'-tagged first ARNA ; (e) copying...
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Stanford University
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Microarray Printhead Return Mechanism
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Currently, the vast majority of contact microarray printheads either use the force of gravity or incorporate springs to return pins to their nominal position. Researchers at Stanford have discovered a novel way to return pins to their nominal position through the elimination of a return force being applied during the application of material to the substrate. ...
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Stanford University
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Microarray-Based DNA Fingerprinting Using Branch Migration Assay
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Stanford researchers have developed a novel method and apparatus for performing DNA fingerprinting using short tandem repeat (STR) analysis and Branch-Migration Assay. The invention uses a microarray platform and can be used with various detection techniques including standard fluorescent labeling or magnetic nanoparticles. ...
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Stanford University
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Minicircle DNA for gene delivery
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Minicircle DNA vectors free of plasmid bacterial DNA sequences are capable of persistent high level of transgene expression in vivo. The minicircle is generated in bacteria from a parental plasmid containing an inducible phage oC31 integrase gene and a therapeutic expression cassette flanked with attB and attP sites. The oC31-mediated intramolecular recombination between attB and attP results in t...
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University of California, Irvine
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Molecular Imprinting for the Recognition of Peptides in Aqueous Solution
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Researchers at the University of California, Irvine, have developed MIPs, wherein the template comprises either a) peptide or amino acid sequence that has an N-terminal histidine or b) histamine. The MIPs were prepared in aqueous systems using reagents that are water soluble at the relevant concentrations. The technology covers methods for using MIPs as receptors or adsorbents for, or to determine...
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Stanford University
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Multiplex Pyrosequencing for typing
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This invention refers to the use of more than one primer in sequencing-by-synthesis reaction system to obtain a fingerprint, which is unique for each genotype to be analyzed. Using this strategy, the analysis time can be shortened, the cost will be decreased and an accurate data will be obtained since each pattern will contain more than one unique peak for each genotype. The strategy can be used f...
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Stanford University
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Nanotubes for Drug Delivery and Selective Cancer Cell Destruction
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This invention introduces a new method for drug delivery and cancer therapy using single wall nanotubes. Specifically, the transport and delivery capabilities of carbon nanotubes can be applied for various biological cargoes. The intrinsic optical property of SWNT can be tuned to trigger cargo release or cell killing. Functionalization of the nanotubes with tumor markers can lead to the applicatio...
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Stanford University
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New Fluorescent Deoxyribosides and their Incorporation into Combinatorial Fluorophore Arrays
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This invention consists of combinatorial arrays of fluorophores (CFAs) built on a repeating oligomeric (e.g.,DNA) backbone. With the DNA backbone, the invention starts with a number of synthesized new fluorescent monomer molecules in which the fluorescent part replaces a DNA base (termed "fluorosides"). By assembling oligomers in various combinations, hundreds or thousands of different fluorescent...
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University of California, Berkeley
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NEW RICE GENE OsEMF1
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The transition from a rosette to an early inflorescence is considered to be the transition from vegetative to reproductive state. This transition is regulated by many flowering genes, both floral repressing and floral promoting. In particular, two Embryonic Flower (EMF1 and EMF2) genes have been identified in Arabidopsis that have been shown to be involved in the process of floral repression. Expr...
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University of California, Berkeley
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NEW RICE GENE OsEMF1
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The transition from a rosette to an early inflorescence is considered to be the transition from vegetative to reproductive state. This transition is regulated by many flowering genes, both floral repressing and floral promoting. In particular, two Embryonic Flower (EMF1 and EMF2) genes have been identified in Arabidopsis that have been shown to be involved in the process of floral repression. Expr...
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University of California, San Diego
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New Technology for Functional Genomics
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A new method has been developed that will allow functional genomics questions to be addressed under a variety of physiological conditions. The method allows selective enrichment of functional DNA elements, such as promoters/enhancers, replication origins a...
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Stanford University
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NOVEL METHODS TO ENHANCE THE ANTI-TUMOR ACTIVITY ASSOCIATED WITH THE DRUG TAXOL
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Lung cancer is the most common cause of cancer death world-wide. The disease kills approximately 1.3 million people annually. Taxanes, a microtubule poison often referred to as taxol, are currently used as a first line defense with moderate but short-term success for many human cancers, including lung cancer. Unfortunately, many patients develop resistance to the drug. Stanford researchers identif...
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Stanford University
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On-chip Electrophoretic Signal Enhancement Using Field-amplified Sample Stacking
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On-chip capillary electrophoresis (CE) devices offer the potential to create portable laboratories on a chip that will enable massive parallel drug discovery, biological weapon detection, fundamental genetics research and proteomics to be done rapidly and on a smaller scale. Such on-chip electrophoresis devices offer reduced sample volumes, opportunities for parallelization, ease of automation, an...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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Photosynthetic Hydrogen Production Using Algae
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Hydrogen gas is considered to be the ideal fuel for combating environmental degradation. However, the biggest obstacle to hydrogen replacing petroleum as the world's primary source of energy is the high cost of cleanly producing this gas. The most cost-effective current method for producing H2 is to use nuclear energy -- but that has environmental issues. Likewise, using solar power is not cost-ef...
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University of California, Berkeley
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PLANT GENES INVOLVED IN THE RESPONSE TO WOUNDING
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Wounding is a common injury occurring to plants as a result of mechanical stresses such as wind, hail, and cultivation and of biotic factors such as insect feeding. Wounding not only directly damages a plant but also provides a site for pathogen entry. As a result, plants have evolved mechanisms to integrate the wound response with pathogen responses. Wounding and disease responses share a number ...
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University of California, Berkeley
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PLANT GENES INVOLVED IN THE RESPONSE TO WOUNDING
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Wounding is a common injury occurring to plants as a result of mechanical stresses such as wind, hail, and cultivation and of biotic factors such as insect feeding. Wounding not only directly damages a plant but also provides a site for pathogen entry. As a result, plants have evolved mechanisms to integrate the wound response with pathogen responses. Wounding and disease responses share a number ...
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University of California, Berkeley
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PLANT GENES INVOLVED IN THE RESPONSE TO WOUNDING
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Wounding is a common injury occurring to plants as a result of mechanical stresses such as wind, hail, and cultivation and of biotic factors such as insect feeding. Wounding not only directly damages a plant but also provides a site for pathogen entry. As a result, plants have evolved mechanisms to integrate the wound response with pathogen responses. Wounding and disease responses share a number ...
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Stanford University
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Population Clustering through Density-Based Merging
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This invention is a method to sort through and analyze large data sets by creating clusters of data. The algorithm intakes data and groups them into clusters, groupings or populations of data. This can be used to analyze data in areas like flow cytometry, marketing, and any other field that contains clusterable parameters. ...
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Stanford University
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Prediction of Protein Side-chain Conformation by Packing Optimization
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This invention is a method for predicting the three-dimensional conformation of a peptide. It utilizes the understanding that amino acid sidechains of a peptide adopt conformations that maximize favorable atom-atom contacts and minimize unfavorable contacts. It determines the energy of the atom-atom interactions and adjusts the amino acid side chain conformations to minimize this energy. ...
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Stanford University
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Quenched DNA probes that "light up" on sensing genetic sequences
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The "light-up" technology is a molecular approach to generating a fluorescent signal on formation of a chemical bond. It is especially useful when applied to DNA probes. "Light-up" probes are essentially nonfluorescent, until they react with another probe to form a longer probe. An increasing fluorescent signal reports on the reaction in real time. This fluorescent signal combined with a chemical ...
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Stanford University
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RabGEF-1 (rin2, Rabex-5), a Novel Inhibitor of Ras-mediated Signaling
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Prof. Stephen Galli and his colleagues at Stanford University have identified and discovered that RabGEF-1 functions as a novel negative regulator/effector of Ras-mediated cell signaling and functional responses during cell activation.Ras proteins are small GTP-binding proteins important in the control of cell activation, proliferation and differentiation in diverse cell types. Ras regulates a wid...
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Stanford University
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Random Homozygous Gene Inactivation Using Expressed Sequence Tag (EST) Libraries
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This invention addresses the important need for unincumbered and efficient approaches to identify the biological functions of genes in eukaryotic cells by utilizing expressed sequence tag (EST) libraries to achieve gene inactivation.Gene expression in antisense orientation is an effective way to suppress the activity and thus the function of target genes. Previous studies that exploited antisense ...
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Stanford University
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Real-time PCR Quantification
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Researchers at Stanford have developed an objective method for quantifying qRT-PCR results using calculations based on the kinetics of individual PCR reactions without the need of the standard curve, independent of any assumptions or subjective judgments which allow direct calculation of efficiency and CT.Quantitative real-time polymerase chain reactions (qRT-PCR) have become the method of choice ...
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Stanford University
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Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing
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RNA interference (RNAi) is a powerful method for silencing the expression of specific genes in diverse plant and animal cells. RNAi is mediated by 21-23 nucleotide small interfering RNAs (siRNAs), which are produced in vivo when Dicer, an RNase III-family enzyme, cleaves larger double-stranded RNAs (dsRNAs). siRNAs, but not large dsRNAs (>30 base pairs), can be used to silence gene expression i...
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Stanford University
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Representational Fragment Amplification (RFA)
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Microarray and diagnostic applications need a reliable method of accurate sample preparation in order to improve the quality of assay results. A method for the non-preferential amplification of a population of nucleic acids (genomic DNA, cDNA, or RNA) has been developed by Stanford researchers, which allows for at least 100,000 fold amplification of a nucleic acid population while maintaining the ...
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Stanford University
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Restriction enzyme-mediated method to generate siRNA vectors and libraries (REGS method)
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RNA interference (RNAi) has become a powerful tool to specifically knockout a gene of interest, whereby endogenous mRNA molecules are specifically targeted for intracellular destruction by the introduction of double-stranded RNA with complementary sequence (dsRNA). In mammalian cells, stable RNAi is commonly achieved by the expression of short hairpin RNA (shRNA) molecules, which are single-strand...
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Stanford University
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Screening Molecular Imaging Probes Using MALDI-TOF-MS
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Researchers at Stanford have discovered a method to do high-throughput screening of molecular imaging probes using matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS). Existing strategies require preparation of radioactively labeled probes even before any evaluation of biological activity is done, which is time consuming and expensive.This method requires th...
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Stanford University
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Significance Analysis of Microarrays (SAM)
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June 2005: A new version of SAM (version 2.0) is now available! This is our first major update of SAM since its initial release 4 years ago.New features include:time course analysisnon-parametric testspattern discoverylocal false discovery ratesmiss ratesFor more information on the new release, please visit the SAM web page at http://www-stat.stanford.edu/~tibs/SAMDESCRIPTIONSAM (Significance Anal...
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Stanford University
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Small molecule probes that bind covalently to protein targets
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Stanford researchers have developed small molecule compounds and methods that can be used to screen cells for kinase proteins. These tools are particularly useful for detecting protein kinases involved in sensing and signaling DNA damage, but can also be utilized for evaluating lipid kinases. Many of the kinases in this class have been implicated in cancer. Although the poor selectivity wortmannin...
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Stanford University
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Stanford Microarray Technology
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In the ten years since researchers in Dr. Pat Browns laboratory at Stanford first described their DNA microarray technology, the invention has established itself as an invaluable tool for studying the expression of thousands of genes simultaneously. The family of patents for this inexpensive technique for assembling slides of parallel nucleic acids for high throughput DNA hybridization assays is n...
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Stanford University
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System for Proteomic Analysis and Drug Discovery
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In an undertaking larger than the human genome project, academic and commercial scientists will analyze the vast array of proteins found in human systems, tissues, and cells. In addition to understanding the human proteome, commercial scientists will utilize improved systems for "many-to-many analysis" to identify which chemical entities bind cellular biomolecules.This array technology identifies ...
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Stanford University
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Universal Linkers for DNA that Release or Transfer Chemical Agents
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The invention provides compositions and methods for the preparation of universal linkers, which are used to modify polynucleotide probes in ligation reactions as well as transfer reactions. The universal linkers typically comprise a functional group, which is linked to the polynucleotide through an activating leaving group and a tether. Such functional groups provide for detectable or functional c...
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University of California, Irvine
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Unnatural Amino Acids That Mimic Peptide Beta-Strands
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Researchers at the University of California, Irvine, have synthesized a non-natural amino acid. This amino acid and its derivatives mimic tripeptide beta-strands. When incorporated into peptides, peptidomimetics or proteins all three types of structures will dimerize by means of beta-sheet interactions. A logical extension of this work is to use this amino acid in agents designed to block the beta...
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Stanford University
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Use of Bayesian Networks for Modeling Cell Signaling Systems from Multiparameter Single-Cell Data
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The Stanford researchers Nolan, Perez, Sachs and collaborators have developed an entirely novel computational technique to extract and reconstruct signaling pathways from high-throughput, multiparameter and simultaneous phospho-proteomic single-cell measurements in human T lymphocytes by using Bayesian networks. Bayesian networks are a form of graphical models to represent probabilistic dependence...
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Stanford University
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Versatile Microarray Platform
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Researchers at the Monterey Bay Aquarium Research Institute (MBARI) have developed a novel microarray platform for generating probe arrays for detection of multiple target sequences simultaneously in a single sample. Nucleic acid probes are attached onto a solid support that can be used in lateral and/or transverse flow assay formats. Printed arrays are suitable for use with unpurified sample homo...
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University of California, Irvine
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Yeast Retrotransposons as a Model to Study HIV and Screen for HIV Anti-Retro Therapeutics
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From a screen of 4,457 S. cerevisae knockout strains, University of California, Irvine (UCI) researchers have discovered over one hundred host factor genes that affect the replication of the retrovirus-like element Ty3. Of these, 64 exhibited increased and 66 decreased Ty3 transposition compared with the parental strain. Previous studies for Ty host factors have reported a large number of genes, i...
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